class DBS3Reader(object):
"""
_DBSReader_
General API for reading data from DBS
"""
# cache all the datatiers known by DBS
_datatiers = {}
def __init__(self, url, logger=None, **contact):
# instantiate dbs api object
try:
self.dbsURL = url
self.dbs = DbsApi(url, **contact)
self.logger = logger or logging.getLogger(self.__class__.__name__)
except dbsClientException as ex:
msg = "Error in DBSReader with DbsApi\n"
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
# connection to PhEDEx (Use default endpoint url)
self.phedex = PhEDEx(responseType="json", dbsUrl=self.dbsURL)
def _getLumiList(self, blockName=None, lfns=None, validFileOnly=1):
"""
currently only take one lfn but dbs api need be updated
"""
try:
if blockName:
lumiLists = self.dbs.listFileLumis(block_name=blockName,
validFileOnly=validFileOnly)
elif lfns:
lumiLists = []
for slfn in grouper(lfns, 50):
lumiLists.extend(
self.dbs.listFileLumiArray(logical_file_name=slfn))
else:
# shouldn't call this with both blockName and lfns empty
# but still returns empty dict for that case
return {}
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listFileLumiArray(%s)\n" % lfns
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
lumiDict = {}
for lumisItem in lumiLists:
lumiDict.setdefault(lumisItem['logical_file_name'], [])
item = {}
item["RunNumber"] = lumisItem['run_num']
item['LumiSectionNumber'] = lumisItem['lumi_section_num']
if lumisItem.get('event_count', None) is not None:
item['EventCount'] = lumisItem['event_count']
lumiDict[lumisItem['logical_file_name']].append(item)
# TODO: add key for lumi and event pair.
return lumiDict
def checkDBSServer(self):
"""
check whether dbs server is up and running
returns {"dbs_instance": "prod/global", "dbs_version": "3.3.144"}
"""
try:
return self.dbs.serverinfo()
except dbsClientException as ex:
msg = "Error in "
msg += "DBS server is not up: %s" % self.dbsURL
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
def listPrimaryDatasets(self, match='*'):
"""
_listPrimaryDatasets_
return a list of primary datasets, The full dataset name must be provided
pattern based mathcing is no longer supported.
If no expression is provided, all datasets are returned
"""
try:
result = self.dbs.listPrimaryDatasets(primary_ds_name=match)
except dbsClientException as ex:
msg = "Error in DBSReader.listPrimaryDataset(%s)\n" % match
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
result = [x['primary_ds_name'] for x in result]
return result
def matchProcessedDatasets(self, primary, tier, process):
"""
_matchProcessedDatasets_
return a list of Processed datasets
"""
result = []
try:
datasets = self.dbs.listDatasets(primary_ds_name=primary,
data_tier_name=tier,
detail=True)
except dbsClientException as ex:
msg = "Error in DBSReader.listProcessedDatasets(%s)\n" % primary
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
for dataset in datasets:
dataset = remapDBS3Keys(dataset, processed_ds_name='Name')
dataset['PathList'] = [dataset['dataset']]
if dataset['Name'] == process:
result.append(dataset)
return result
def listRuns(self, dataset=None, block=None):
"""
it gets list of DbsRun object but for our purpose
only list of number is collected.
DbsRun (RunNumber,
NumberOfEvents,
NumberOfLumiSections,
TotalLuminosity,
StoreNumber,
StartOfRungetLong,
EndOfRun,
CreationDate,
CreatedBy,
LastModificationDate,
LastModifiedBy
)
"""
runs = []
try:
if block:
results = self.dbs.listRuns(block_name=block)
else:
results = self.dbs.listRuns(dataset=dataset)
except dbsClientException as ex:
msg = "Error in DBSReader.listRuns(%s, %s)\n" % (dataset, block)
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
[runs.extend(x['run_num']) for x in results]
return runs
def listRunLumis(self, dataset=None, block=None):
"""
It gets a list of DBSRun objects and returns the number of lumisections per run
DbsRun (RunNumber,
NumberOfEvents,
NumberOfLumiSections,
TotalLuminosity,
StoreNumber,
StartOfRungetLong,
EndOfRun,
CreationDate,
CreatedBy,
LastModificationDate,
LastModifiedBy
)
"""
# Pointless code in python3
if isinstance(block, str):
block = unicode(block)
if isinstance(dataset, str):
dataset = unicode(dataset)
try:
if block:
results = self.dbs.listRuns(block_name=block)
else:
results = self.dbs.listRuns(dataset=dataset)
except dbsClientException as ex:
msg = "Error in DBSReader.listRuns(%s, %s)\n" % (dataset, block)
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
# send runDict format as result, this format is for sync with dbs2 call
# which has {run_number: num_lumis} but dbs3 call doesn't return num Lumis
# So it returns {run_number: None}
# TODO: After DBS2 is completely removed change the return format more sensible one
runDict = {}
for x in results:
for runNumber in x["run_num"]:
runDict[runNumber] = None
return runDict
def listProcessedDatasets(self, primary, dataTier='*'):
"""
_listProcessedDatasets_
return a list of Processed datasets for the primary and optional
data tier value
"""
try:
result = self.dbs.listDatasets(primary_ds_name=primary,
data_tier_name=dataTier)
except dbsClientException as ex:
msg = "Error in DBSReader.listProcessedDatasets(%s)\n" % primary
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
result = [x['dataset'].split('/')[2] for x in result]
return result
def listDatasetFiles(self, datasetPath):
"""
_listDatasetFiles_
Get list of files for dataset
"""
return [
x['logical_file_name']
for x in self.dbs.listFileArray(dataset=datasetPath)
]
@staticmethod
def listDatatiers(dbsUrl=None):
"""
_listDatatiers_
Get a list of datatiers known by DBS.
"""
if dbsUrl is None:
msg = "Error in DBSReader.listDatatiers(). DBS Url not set."
raise DBSReaderError(msg)
timenow = int(time.time())
if DBS3Reader._datatiers and timenow - 7200 < DBS3Reader._datatiers[
'ts']:
return DBS3Reader._datatiers['tiers']
try:
DBS3Reader._setDatatiersCache(timenow, dbsUrl)
except Exception as ex:
if not DBS3Reader._datatiers:
msg = "Error in DBSReader.listDatatiers\n%s" % formatEx3(ex)
raise DBSReaderError(msg)
return DBS3Reader._datatiers['tiers']
@staticmethod
def _setDatatiersCache(ts, dbsUrl):
"""
Set a timestamp and update the list of datatiers cached in
the class property
"""
dbs = DbsApi(dbsUrl)
DBS3Reader._datatiers['ts'] = ts
DBS3Reader._datatiers['tiers'] = [
tier['data_tier_name'] for tier in dbs.listDataTiers()
]
return
def listDatasetFileDetails(self,
datasetPath,
getParents=False,
getLumis=True,
validFileOnly=1):
"""
TODO: This is completely wrong need to be redone. or be removed - getting dataset altogether
might be to costly
_listDatasetFileDetails_
Get list of lumis, events, and parents for each file in a dataset
Return a dict where the keys are the files, and for each file we have something like:
{ 'NumberOfEvents': 545,
'BlockName': '/HighPileUp/Run2011A-v1/RAW#dd6e0796-cbcc-11e0-80a9-003048caaace',
'Lumis': {173658: [8, 12, 9, 14, 19, 109, 105]},
'Parents': [],
'Checksum': '22218315',
'Adler32': 'a41a1446',
'FileSize': 286021145,
'ValidFile': 1
}
"""
fileDetails = self.getFileListByDataset(dataset=datasetPath,
validFileOnly=validFileOnly,
detail=True)
blocks = set() # the set of blocks of the dataset
# Iterate over the files and prepare the set of blocks and a dict where the keys are the files
files = {}
for f in fileDetails:
blocks.add(f['block_name'])
files[f['logical_file_name']] = remapDBS3Keys(f, stringify=True)
files[f['logical_file_name']]['ValidFile'] = f['is_file_valid']
files[f['logical_file_name']]['Lumis'] = {}
files[f['logical_file_name']]['Parents'] = []
# Iterate over the blocks and get parents and lumis
for blockName in blocks:
# get the parents
if getParents:
parents = self.dbs.listFileParents(block_name=blockName)
for p in parents:
if p['logical_file_name'] in files: # invalid files are not there if validFileOnly=1
files[p['logical_file_name']]['Parents'].extend(
p['parent_logical_file_name'])
if getLumis:
# get the lumis
file_lumis = self.dbs.listFileLumis(block_name=blockName)
for f in file_lumis:
if f['logical_file_name'] in files: # invalid files are not there if validFileOnly=1
if f['run_num'] in files[
f['logical_file_name']]['Lumis']:
files[f['logical_file_name']]['Lumis'][
f['run_num']].extend(f['lumi_section_num'])
else:
files[f['logical_file_name']]['Lumis'][
f['run_num']] = f['lumi_section_num']
return files
def crossCheck(self, datasetPath, *lfns):
"""
_crossCheck_
For the dataset provided, check that the lfns listed all exist
in the dataset.
Return the list of lfns that are in the dataset
"""
allLfns = self.dbs.listFileArray(dataset=datasetPath,
validFileOnly=1,
detail=False)
setOfAllLfns = set(allLfns)
setOfKnownLfns = set(lfns)
return list(setOfAllLfns.intersection(setOfKnownLfns))
def crossCheckMissing(self, datasetPath, *lfns):
"""
_crossCheckMissing_
As cross check, but return value is a list of files that
are *not* known by DBS
"""
allLfns = self.dbs.listFileArray(dataset=datasetPath,
validFileOnly=1,
detail=False)
setOfAllLfns = set(allLfns)
setOfKnownLfns = set(lfns)
knownFiles = setOfAllLfns.intersection(setOfKnownLfns)
unknownFiles = setOfKnownLfns.difference(knownFiles)
return list(unknownFiles)
def getDBSSummaryInfo(self, dataset=None, block=None):
"""
Get dataset summary includes # of files, events, blocks and total size
"""
# FIXME: Doesnt raise exceptions on missing data as old api did
if dataset:
self.checkDatasetPath(dataset)
try:
if block:
summary = self.dbs.listFileSummaries(block_name=block,
validFileOnly=1)
else: # dataset case dataset shouldn't be None
summary = self.dbs.listFileSummaries(dataset=dataset,
validFileOnly=1)
except Exception as ex:
msg = "Error in DBSReader.getDBSSummaryInfo(%s, %s)\n" % (dataset,
block)
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if not summary or summary[0].get(
'file_size') is None: # appears to indicate missing dataset
msg = "DBSReader.listDatasetSummary(%s, %s): No matching data"
raise DBSReaderError(msg % (dataset, block))
result = remapDBS3Keys(summary[0], stringify=True)
result['path'] = dataset if dataset else ''
result['block'] = block if block else ''
return result
def getFileBlocksInfo(self,
dataset,
onlyClosedBlocks=False,
blockName=None,
locations=True):
"""
"""
self.checkDatasetPath(dataset)
args = {'dataset': dataset, 'detail': True}
if blockName:
args['block_name'] = blockName
try:
blocks = self.dbs.listBlocks(**args)
except Exception as ex:
msg = "Error in DBSReader.getFileBlocksInfo(%s)\n" % dataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
blocks = [
remapDBS3Keys(block, stringify=True, block_name='Name')
for block in blocks
]
# only raise if blockName not specified - mimic dbs2 error handling
if not blocks and not blockName:
msg = "DBSReader.getFileBlocksInfo(%s, %s): No matching data"
raise DBSReaderError(msg % (dataset, blockName))
if locations:
for block in blocks:
block['PhEDExNodeList'] = [{
'Name': x
} for x in self.listFileBlockLocation(block['Name'])]
if onlyClosedBlocks:
return [x for x in blocks if str(x['OpenForWriting']) != "1"]
return blocks
def listFileBlocks(self, dataset, onlyClosedBlocks=False, blockName=None):
"""
_listFileBlocks_
Retrieve a list of fileblock names for a dataset
"""
self.checkDatasetPath(dataset)
args = {'dataset': dataset, 'detail': False}
if blockName:
args['block_name'] = blockName
if onlyClosedBlocks:
args['detail'] = True
try:
blocks = self.dbs.listBlocks(**args)
except dbsClientException as ex:
msg = "Error in DBSReader.listFileBlocks(%s)\n" % dataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if onlyClosedBlocks:
result = [
x['block_name'] for x in blocks
if str(x['open_for_writing']) != "1"
]
else:
result = [x['block_name'] for x in blocks]
return result
def listOpenFileBlocks(self, dataset):
"""
_listOpenFileBlocks_
Retrieve a list of open fileblock names for a dataset
"""
self.checkDatasetPath(dataset)
try:
blocks = self.dbs.listBlocks(dataset=dataset, detail=True)
except dbsClientException as ex:
msg = "Error in DBSReader.listFileBlocks(%s)\n" % dataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
result = [
x['block_name'] for x in blocks
if str(x['open_for_writing']) == "1"
]
return result
def blockExists(self, fileBlockName):
"""
_blockExists_
Check to see if block with name provided exists in the DBS
Instance.
Return True if exists, False if not
"""
self.checkBlockName(fileBlockName)
try:
blocks = self.dbs.listBlocks(block_name=fileBlockName)
except Exception as ex:
msg = "Error in "
msg += "DBSReader.blockExists(%s)\n" % fileBlockName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if len(blocks) == 0:
return False
return True
def listFilesInBlock(self, fileBlockName, lumis=True, validFileOnly=1):
"""
_listFilesInBlock_
Get a list of files in the named fileblock
TODO: lumis can be false when lumi splitting is not required
However WMBSHelper expect file['LumiList'] to get the run number
so for now it will be always true.
We need to clean code up when dbs2 is completely deprecated.
calling lumis for run number is expensive.
"""
if not self.blockExists(fileBlockName):
msg = "DBSReader.listFilesInBlock(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
try:
files = self.dbs.listFileArray(block_name=fileBlockName,
validFileOnly=validFileOnly,
detail=True)
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listFilesInBlock(%s)\n" % fileBlockName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if lumis:
lumiDict = self._getLumiList(blockName=fileBlockName,
validFileOnly=validFileOnly)
result = []
for fileInfo in files:
if lumis:
fileInfo["LumiList"] = lumiDict[fileInfo['logical_file_name']]
result.append(remapDBS3Keys(fileInfo, stringify=True))
return result
def listFilesInBlockWithParents(self,
fileBlockName,
lumis=True,
validFileOnly=1):
"""
_listFilesInBlockWithParents_
Get a list of files in the named fileblock including
the parents of that file.
TODO: lumis can be false when lumi splitting is not required
However WMBSHelper expect file['LumiList'] to get the run number
so for now it will be always true.
"""
if not self.blockExists(fileBlockName):
msg = "DBSReader.listFilesInBlockWithParents(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
try:
# TODO: shoud we get only valid block for this?
files = self.dbs.listFileParents(block_name=fileBlockName)
fileDetails = self.listFilesInBlock(fileBlockName, lumis,
validFileOnly)
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listFilesInBlockWithParents(%s)\n" % (
fileBlockName, )
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
childByParents = defaultdict(list)
for f in files:
# Probably a child can have more than 1 parent file
for fp in f['parent_logical_file_name']:
childByParents[fp].append(f['logical_file_name'])
parentsLFNs = childByParents.keys()
if len(parentsLFNs) == 0:
msg = "Error in "
msg += "DBSReader.listFilesInBlockWithParents(%s)\n There is no parents files" % (
fileBlockName)
raise DBSReaderError(msg)
parentFilesDetail = []
# TODO: slicing parentLFNs util DBS api is handling that.
# Remove slicing if DBS api handles
for pLFNs in grouper(parentsLFNs, 50):
parentFilesDetail.extend(
self.dbs.listFileArray(logical_file_name=pLFNs, detail=True))
if lumis:
parentLumis = self._getLumiList(lfns=parentsLFNs)
parentsByLFN = defaultdict(list)
for pf in parentFilesDetail:
parentLFN = pf['logical_file_name']
dbsFile = remapDBS3Keys(pf, stringify=True)
if lumis:
dbsFile["LumiList"] = parentLumis[parentLFN]
for childLFN in childByParents[parentLFN]:
parentsByLFN[childLFN].append(dbsFile)
for fileInfo in fileDetails:
fileInfo["ParentList"] = parentsByLFN[
fileInfo['logical_file_name']]
return fileDetails
def lfnsInBlock(self, fileBlockName):
"""
_lfnsInBlock_
LFN list only for block, details = False => faster query
"""
if not self.blockExists(fileBlockName):
msg = "DBSReader.lfnsInBlock(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
try:
lfns = self.dbs.listFileArray(block_name=fileBlockName,
validFileOnly=1,
detail=False)
return lfns
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listFilesInBlock(%s)\n" % fileBlockName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
def listFileBlockLocation(self, fileBlockNames, dbsOnly=False):
"""
_listFileBlockLocation_
Get origin_site_name of a block
"""
singleBlockName = None
if isinstance(fileBlockNames, basestring):
singleBlockName = fileBlockNames
fileBlockNames = [fileBlockNames]
for block in fileBlockNames:
self.checkBlockName(block)
locations = {}
node_filter = set(['UNKNOWN', None])
if dbsOnly:
blocksInfo = {}
try:
for block in fileBlockNames:
blocksInfo.setdefault(block, [])
# there should be only one element with a single origin site string ...
for blockInfo in self.dbs.listBlockOrigin(
block_name=block):
blocksInfo[block].append(blockInfo['origin_site_name'])
except dbsClientException as ex:
msg = "Error in DBS3Reader: self.dbs.listBlockOrigin(block_name=%s)\n" % fileBlockNames
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
else:
try:
blocksInfo = self.phedex.getReplicaPhEDExNodesForBlocks(
block=fileBlockNames, complete='y')
except Exception as ex:
msg = "Error while getting block location from PhEDEx for block_name=%s)\n" % fileBlockNames
msg += "%s\n" % str(ex)
raise Exception(msg)
for block in fileBlockNames:
valid_nodes = set(blocksInfo.get(block, [])) - node_filter
locations[block] = list(valid_nodes)
# returning single list if a single block is passed
if singleBlockName:
return locations[singleBlockName]
return locations
def getFileBlock(self, fileBlockName, dbsOnly=False):
"""
_getFileBlock_
dbsOnly flag is mostly meant for StoreResults, since there is no
data in TMDB.
return a dictionary:
{ blockName: {
"PhEDExNodeNames" : [<pnn list>],
"Files" : { LFN : Events },
}
}
"""
# Pointless code in python3
if isinstance(fileBlockName, str):
fileBlockName = unicode(fileBlockName)
if not self.blockExists(fileBlockName):
msg = "DBSReader.getFileBlock(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
result = {
fileBlockName: {
"PhEDExNodeNames":
self.listFileBlockLocation(fileBlockName, dbsOnly),
"Files":
self.listFilesInBlock(fileBlockName),
"IsOpen":
self.blockIsOpen(fileBlockName)
}
}
return result
def getFileBlockWithParents(self, fileBlockName):
"""
_getFileBlockWithParents_
return a dictionary:
{ blockName: {
"PhEDExNodeNames" : [<pnn list>],
"Files" : dictionaries representing each file
}
}
files
"""
if isinstance(fileBlockName, str):
fileBlockName = unicode(fileBlockName)
if not self.blockExists(fileBlockName):
msg = "DBSReader.getFileBlockWithParents(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
result = {
fileBlockName: {
"PhEDExNodeNames": self.listFileBlockLocation(fileBlockName),
"Files": self.listFilesInBlockWithParents(fileBlockName),
"IsOpen": self.blockIsOpen(fileBlockName)
}
}
return result
def getFiles(self, dataset, onlyClosedBlocks=False):
"""
_getFiles_
Returns a dictionary of block names for the dataset where
each block constists of a dictionary containing the PhEDExNodeNames
for that block and the files in that block by LFN mapped to NEvents
"""
result = {}
blocks = self.listFileBlocks(dataset, onlyClosedBlocks)
[result.update(self.getFileBlock(x)) for x in blocks]
return result
def listBlockParents(self, blockName):
"""Get parent blocks for block"""
result = []
self.checkBlockName(blockName)
blocks = self.dbs.listBlockParents(block_name=blockName)
for block in blocks:
toreturn = {'Name': block['parent_block_name']}
toreturn['PhEDExNodeList'] = self.listFileBlockLocation(
toreturn['Name'])
result.append(toreturn)
return result
def blockIsOpen(self, blockName):
"""
_blockIsOpen_
Return True if named block is open, false if not, or if block
doenst exist
"""
self.checkBlockName(blockName)
blockInstance = self.dbs.listBlocks(block_name=blockName, detail=True)
if len(blockInstance) == 0:
return False
blockInstance = blockInstance[0]
isOpen = blockInstance.get('open_for_writing', 1)
if isOpen == 0:
return False
return True
def blockToDatasetPath(self, blockName):
"""
_blockToDatasetPath_
Given a block name, get the dataset Path associated with that
Block.
Returns the dataset path, or None if not found
"""
self.checkBlockName(blockName)
try:
blocks = self.dbs.listBlocks(block_name=blockName, detail=True)
except Exception as ex:
msg = "Error in "
msg += "DBSReader.blockToDatasetPath(%s)\n" % blockName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if blocks == []:
return None
pathname = blocks[-1].get('dataset', None)
return pathname
def listDatasetLocation(self, datasetName, dbsOnly=False):
"""
_listDatasetLocation_
List the origin SEs where there is at least a block of the given
dataset.
"""
self.checkDatasetPath(datasetName)
locations = set()
if dbsOnly:
try:
blocksInfo = self.dbs.listBlockOrigin(dataset=datasetName)
except dbsClientException as ex:
msg = "Error in DBSReader: dbsApi.listBlocks(dataset=%s)\n" % datasetName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if not blocksInfo: # no data location from dbs
return list()
for blockInfo in blocksInfo:
locations.update(blockInfo['origin_site_name'])
locations.difference_update(
['UNKNOWN', None]) # remove entry when SE name is 'UNKNOWN'
else:
try:
blocksInfo = self.phedex.getReplicaPhEDExNodesForBlocks(
dataset=[datasetName], complete='y')
except Exception as ex:
msg = "Error while getting block location from PhEDEx for dataset=%s)\n" % datasetName
msg += "%s\n" % str(ex)
raise Exception(msg)
if blocksInfo:
for blockSites in blocksInfo.values():
locations.update(blockSites)
return list(locations)
def checkDatasetPath(self, pathName):
"""
_checkDatasetPath_
"""
if pathName in ("", None):
raise DBSReaderError("Invalid Dataset Path name: => %s <=" %
pathName)
else:
try:
result = self.dbs.listDatasets(dataset=pathName,
dataset_access_type='*')
if len(result) == 0:
raise DBSReaderError("Dataset %s doesn't exist in DBS %s" %
(pathName, self.dbsURL))
except (dbsClientException, HTTPError) as ex:
msg = "Error in "
msg += "DBSReader.checkDatasetPath(%s)\n" % pathName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
return
def checkBlockName(self, blockName):
"""
_checkBlockName_
"""
if blockName in ("", "*", None):
raise DBSReaderError("Invalid Block name: => %s <=" % blockName)
def getFileListByDataset(self, dataset, validFileOnly=1, detail=True):
"""
_getFileListByDataset_
Given a dataset, retrieves all blocks, lfns and number of events (among other
not really important info).
Returns a list of dict.
"""
try:
fileList = self.dbs.listFileArray(dataset=dataset,
validFileOnly=validFileOnly,
detail=detail)
return fileList
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.getFileListByDataset(%s)\n" % dataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
def listDatasetParents(self, childDataset):
"""
list the the parents dataset path given childDataset
"""
try:
parentList = self.dbs.listDatasetParents(dataset=childDataset)
return parentList
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listDatasetParents(%s)\n" % childDataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
# def getListFilesByLumiAndDataset(self, dataset, files):
# "Unsing pycurl to get all the child parents pair for given dataset"
#
# urls = ['%s/data/dbs/fileparentbylumis?block_name=%s' % (
# self.dbsURL, b["block_name"]) for b in self.dbs.listBlocks(dataset=dataset)]
#
# data = multi_getdata(urls, ckey(), cert())
# rdict = {}
# for row in data:
# try:
# data = json.loads(row['data'])
# rdict[req] = data['result'][0] # we get back {'result': [workflow]} dict
# except Exception as exp:
# print("ERROR: fail to load data as json record, error=%s" % str(exp))
# print(row)
# return rdict
def getParentFilesGivenParentDataset(self, parentDataset, childLFNs):
"""
returns parent files for given childLFN when DBS doesn't have direct parent child relationship in DB
Only use this for finding missing parents
:param parentDataset: parent dataset for childLFN
:param childLFN: a file in child dataset
:return: set of parent files for childLFN
"""
fInfo = self.dbs.listFileLumiArray(logical_file_name=childLFNs)
parentFiles = defaultdict(set)
for f in fInfo:
pFileList = self.dbs.listFiles(dataset=parentDataset,
run_num=f['run_num'],
lumi_list=f['lumi_section_num'])
pFiles = set([x['logical_file_name'] for x in pFileList])
parentFiles[f['logical_file_name']] = parentFiles[
f['logical_file_name']].union(pFiles)
return parentFiles
def getParentFilesByLumi(self, childLFN):
"""
get the parent file's lfns by lumi (This might not be the actual parentage relations in DBS just parentage by Lumis).
use for only specific lfn for validating purpose, for the parentage fix use findAndInsertMissingParentage
:param childLFN:
:return: list of dictionary with parent files for given child LFN and parent dataset
[{"ParentDataset": /abc/bad/ddd, "ParentFiles": [alf, baf, ...]]
"""
childDatasets = self.dbs.listDatasets(logical_file_name=childLFN)
result = []
for i in childDatasets:
parents = self.dbs.listDatasetParents(dataset=i["dataset"])
for parent in parents:
parentFiles = self.getParentFilesGivenParentDataset(
parent['parent_dataset'], childLFN)
result.append({
"ParentDataset": parent['parent_dataset'],
"ParentFiles": list(parentFiles)
})
return result
def listParentsByLumi(self, childBlockName, childLFNs=[]):
"""
:param childBlockName: child block name
:param childLFNs: list of child lfns if it is not specified, all the file in the block will be used,
if specified, dbs validate child lfns from the childBlockName
:return: list of list with child and parent id pair. [[1,2], [3,4]...]
"""
return self.dbs.listFileParentsByLumi(block_name=childBlockName,
logical_file_name=childLFNs)
def insertFileParents(self, childBlockName, childParentsIDPairs):
"""
:param childBlockName: child block name
:param childParentsIDPairs: list of list child and parent file ids, i.e. [[1,2], [3,4]...]
dbs validate child ids from the childBlockName
:return: None
"""
return self.dbs.insertFileParents({
"block_name":
childBlockName,
"child_parent_id_list":
childParentsIDPairs
})
def findAndInsertMissingParentage(self,
childBlockName,
childLFNs=[],
insertFlag=True):
"""
:param childBlockName: child block name
:param childLFNs: list of child lfns if it is not specified, all the file in the block will be used,
if specified, dbs validate child lfns from the childBlockName
:return: number of file parents pair inserted
"""
fileParents = self.dbs.listFileParentsByLumi(
block_name=childBlockName, logical_file_name=childLFNs)
childParentsIDPairs = fileParents[0]["child_parent_id_list"]
if insertFlag:
self.dbs.insertFileParents({
"block_name":
childBlockName,
"child_parent_id_list":
childParentsIDPairs
})
return len(childParentsIDPairs)
def listBlocksWithNoParents(self, childDataset):
"""
:param childDataset: child dataset for
:return: set of child blocks with no parentBlock
"""
allBlocks = self.dbs.listBlocks(dataset=childDataset)
blockNames = []
for block in allBlocks:
blockNames.append(block['block_name'])
parentBlocks = self.dbs.listBlockParents(block_name=blockNames)
cblock = set()
for pblock in parentBlocks:
cblock.add(pblock['this_block_name'])
noParentBlocks = set(blockNames) - cblock
return noParentBlocks
def listFilesWithNoParents(self, childBlockName):
"""
:param childBlockName:
:return:
"""
allFiles = self.dbs.listFiles(block_name=childBlockName)
parentFiles = self.dbs.listFileParents(block_name=childBlockName)
allFileNames = set()
for fInfo in allFiles:
allFileNames.add(fInfo['logical_file_name'])
cfile = set()
for pFile in parentFiles:
cfile.add(pFile['logical_file_name'])
noParentFiles = allFileNames - cfile
return list(noParentFiles)
def fixMissingParentageDatasets(self, childDataset, insertFlag=True):
"""
:param childDataset: child dataset need to set the parentage correctly.
:return: blocks which failed to insert parentage. for retry
"""
pDatasets = self.listDatasetParents(childDataset)
# print("parent datasets %s\n" % pDatasets)
# pDatasets format is
# [{'this_dataset': '/SingleMuon/Run2016D-03Feb2017-v1/MINIAOD', 'parent_dataset_id': 13265209, 'parent_dataset': '/SingleMuon/Run2016D-23Sep2016-v1/AOD'}]
if not pDatasets:
self.logger.warning("No parent dataset found for child dataset %s",
childDataset)
return {}
blocks = self.listBlocksWithNoParents(childDataset)
failedBlocks = []
for blockName in blocks:
try:
numFiles = self.findAndInsertMissingParentage(
blockName, insertFlag=insertFlag)
self.logger.debug("%s file parentage added for block %s" %
(numFiles, blockName))
except Exception as ex:
self.logger.exception("Parentage updated failed for block %s",
blockName)
failedBlocks.append(blockName)
return failedBlocks
def insertMissingParentageForAllFiles(self,
childDataset,
filterFilesWithParents=True,
insertFlag=False):
"""
:param childDataset: child dataset need to set the parentage correctly.
:param filterFilesWithParents: if True, only select files without parents, if False all the files in the dataset
:param insertFlag: if True, insert to DBS, if False just get the list of the file parentage without insert
:return: blocks which failed to insert parentage. should be used for retrying
"""
blocks = [
b['block_name'] for b in self.dbs.listBlocks(dataset=childDataset)
]
failedBlocks = []
print("Handling %d blocks" % len(blocks))
totalFiles = 0
for blockName in blocks:
try:
if filterFilesWithParents:
childLFNs = self.listFilesWithNoParents(blockName)
if len(childLFNs) == 0:
continue
else:
childLFNs = []
numFiles = self.findAndInsertMissingParentage(
blockName, childLFNs=childLFNs, insertFlag=insertFlag)
print("%s file parentage added for block %s" %
(numFiles, blockName))
totalFiles += numFiles
except Exception as e:
print(traceback.format_exc())
failedBlocks.append(blockName)
print("Total pairs: ", totalFiles)
return failedBlocks
class DBS3Reader(object):
"""
_DBSReader_
General API for reading data from DBS
"""
def __init__(self, url, logger=None, **contact):
# instantiate dbs api object
try:
self.dbsURL = url.replace("cmsweb.cern.ch", "cmsweb-prod.cern.ch")
self.dbs = DbsApi(self.dbsURL, **contact)
self.logger = logger or logging.getLogger(self.__class__.__name__)
except dbsClientException as ex:
msg = "Error in DBSReader with DbsApi\n"
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
def _getLumiList(self, blockName=None, lfns=None, validFileOnly=1):
"""
currently only take one lfn but dbs api need be updated
"""
try:
if blockName:
lumiLists = self.dbs.listFileLumis(block_name=blockName,
validFileOnly=validFileOnly)
elif lfns:
lumiLists = []
for slfn in grouper(lfns, 50):
lumiLists.extend(
self.dbs.listFileLumiArray(logical_file_name=slfn))
else:
# shouldn't call this with both blockName and lfns empty
# but still returns empty dict for that case
return {}
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listFileLumiArray(%s)\n" % lfns
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
lumiDict = {}
for lumisItem in lumiLists:
lumiDict.setdefault(lumisItem['logical_file_name'], [])
item = {}
item["RunNumber"] = lumisItem['run_num']
item['LumiSectionNumber'] = lumisItem['lumi_section_num']
if lumisItem.get('event_count', None) is not None:
item['EventCount'] = lumisItem['event_count']
lumiDict[lumisItem['logical_file_name']].append(item)
# TODO: add key for lumi and event pair.
return lumiDict
def checkDBSServer(self):
"""
check whether dbs server is up and running
returns {"dbs_instance": "prod/global", "dbs_version": "3.3.144"}
"""
try:
return self.dbs.serverinfo()
except dbsClientException as ex:
msg = "Error in "
msg += "DBS server is not up: %s" % self.dbsURL
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
def listPrimaryDatasets(self, match='*'):
"""
_listPrimaryDatasets_
return a list of primary datasets, The full dataset name must be provided
pattern based mathcing is no longer supported.
If no expression is provided, all datasets are returned
"""
try:
result = self.dbs.listPrimaryDatasets(primary_ds_name=match)
except dbsClientException as ex:
msg = "Error in DBSReader.listPrimaryDataset(%s)\n" % match
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
result = [x['primary_ds_name'] for x in result]
return result
def matchProcessedDatasets(self, primary, tier, process):
"""
_matchProcessedDatasets_
return a list of Processed datasets
"""
result = []
try:
datasets = self.dbs.listDatasets(primary_ds_name=primary,
data_tier_name=tier,
detail=True)
except dbsClientException as ex:
msg = "Error in DBSReader.listProcessedDatasets(%s)\n" % primary
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
for dataset in datasets:
dataset = remapDBS3Keys(dataset, processed_ds_name='Name')
dataset['PathList'] = [dataset['dataset']]
if dataset['Name'] == process:
result.append(dataset)
return result
def listRuns(self, dataset=None, block=None):
"""
it gets list of DbsRun object but for our purpose
only list of number is collected.
DbsRun (RunNumber,
NumberOfEvents,
NumberOfLumiSections,
TotalLuminosity,
StoreNumber,
StartOfRungetLong,
EndOfRun,
CreationDate,
CreatedBy,
LastModificationDate,
LastModifiedBy
)
"""
runs = []
try:
if block:
results = self.dbs.listRuns(block_name=block)
else:
results = self.dbs.listRuns(dataset=dataset)
except dbsClientException as ex:
msg = "Error in DBSReader.listRuns(%s, %s)\n" % (dataset, block)
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
for x in results:
runs.extend(x['run_num'])
return runs
def listRunLumis(self, dataset=None, block=None):
"""
It gets a list of DBSRun objects and returns the number of lumisections per run
DbsRun (RunNumber,
NumberOfEvents,
NumberOfLumiSections,
TotalLuminosity,
StoreNumber,
StartOfRungetLong,
EndOfRun,
CreationDate,
CreatedBy,
LastModificationDate,
LastModifiedBy
)
"""
# Pointless code in python3
block = decodeBytesToUnicode(block)
dataset = decodeBytesToUnicode(dataset)
try:
if block:
results = self.dbs.listRuns(block_name=block)
else:
results = self.dbs.listRuns(dataset=dataset)
except dbsClientException as ex:
msg = "Error in DBSReader.listRuns(%s, %s)\n" % (dataset, block)
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
# send runDict format as result, this format is for sync with dbs2 call
# which has {run_number: num_lumis} but dbs3 call doesn't return num Lumis
# So it returns {run_number: None}
# TODO: After DBS2 is completely removed change the return format more sensible one
runDict = {}
for x in results:
for runNumber in x["run_num"]:
runDict[runNumber] = None
return runDict
def listProcessedDatasets(self, primary, dataTier='*'):
"""
_listProcessedDatasets_
return a list of Processed datasets for the primary and optional
data tier value
"""
try:
result = self.dbs.listDatasets(primary_ds_name=primary,
data_tier_name=dataTier)
except dbsClientException as ex:
msg = "Error in DBSReader.listProcessedDatasets(%s)\n" % primary
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
result = [x['dataset'].split('/')[2] for x in result]
return result
def listDatasetFiles(self, datasetPath):
"""
_listDatasetFiles_
Get list of files for dataset
"""
return [
x['logical_file_name']
for x in self.dbs.listFileArray(dataset=datasetPath)
]
def listDatatiers(self):
"""
_listDatatiers_
Get a list of datatiers known by DBS.
"""
return [tier['data_tier_name'] for tier in self.dbs.listDataTiers()]
def listDatasetFileDetails(self,
datasetPath,
getParents=False,
getLumis=True,
validFileOnly=1):
"""
TODO: This is completely wrong need to be redone. or be removed - getting dataset altogether
might be to costly
_listDatasetFileDetails_
Get list of lumis, events, and parents for each file in a dataset
Return a dict where the keys are the files, and for each file we have something like:
{ 'NumberOfEvents': 545,
'BlockName': '/HighPileUp/Run2011A-v1/RAW#dd6e0796-cbcc-11e0-80a9-003048caaace',
'Lumis': {173658: [8, 12, 9, 14, 19, 109, 105]},
'Parents': [],
'Checksum': '22218315',
'Adler32': 'a41a1446',
'FileSize': 286021145,
'ValidFile': 1
}
"""
fileDetails = self.getFileListByDataset(dataset=datasetPath,
validFileOnly=validFileOnly,
detail=True)
blocks = set() # the set of blocks of the dataset
# Iterate over the files and prepare the set of blocks and a dict where the keys are the files
files = {}
for f in fileDetails:
blocks.add(f['block_name'])
files[f['logical_file_name']] = remapDBS3Keys(f, stringify=True)
files[f['logical_file_name']]['ValidFile'] = f['is_file_valid']
files[f['logical_file_name']]['Lumis'] = {}
files[f['logical_file_name']]['Parents'] = []
# Iterate over the blocks and get parents and lumis
for blockName in blocks:
# get the parents
if getParents:
parents = self.dbs.listFileParents(block_name=blockName)
for p in parents:
if p['logical_file_name'] in files: # invalid files are not there if validFileOnly=1
files[p['logical_file_name']]['Parents'].extend(
p['parent_logical_file_name'])
if getLumis:
# get the lumis
file_lumis = self.dbs.listFileLumis(block_name=blockName)
for f in file_lumis:
if f['logical_file_name'] in files: # invalid files are not there if validFileOnly=1
if f['run_num'] in files[
f['logical_file_name']]['Lumis']:
files[f['logical_file_name']]['Lumis'][
f['run_num']].extend(f['lumi_section_num'])
else:
files[f['logical_file_name']]['Lumis'][
f['run_num']] = f['lumi_section_num']
return files
def crossCheck(self, datasetPath, *lfns):
"""
_crossCheck_
For the dataset provided, check that the lfns listed all exist
in the dataset.
Return the list of lfns that are in the dataset
"""
allLfns = self.dbs.listFileArray(dataset=datasetPath,
validFileOnly=1,
detail=False)
setOfAllLfns = set(allLfns)
setOfKnownLfns = set(lfns)
return list(setOfAllLfns.intersection(setOfKnownLfns))
def crossCheckMissing(self, datasetPath, *lfns):
"""
_crossCheckMissing_
As cross check, but return value is a list of files that
are *not* known by DBS
"""
allLfns = self.dbs.listFileArray(dataset=datasetPath,
validFileOnly=1,
detail=False)
setOfAllLfns = set(allLfns)
setOfKnownLfns = set(lfns)
knownFiles = setOfAllLfns.intersection(setOfKnownLfns)
unknownFiles = setOfKnownLfns.difference(knownFiles)
return list(unknownFiles)
def getDBSSummaryInfo(self, dataset=None, block=None):
"""
Get dataset summary includes # of files, events, blocks and total size
"""
if dataset:
self.checkDatasetPath(dataset)
try:
if block:
summary = self.dbs.listFileSummaries(block_name=block,
validFileOnly=1)
else:
summary = self.dbs.listFileSummaries(dataset=dataset,
validFileOnly=1)
except Exception as ex:
msg = "Error in DBSReader.getDBSSummaryInfo(%s, %s)\n" % (dataset,
block)
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if not summary: # missing data or all files invalid
return {}
result = remapDBS3Keys(summary[0], stringify=True)
result['path'] = dataset if dataset else ''
result['block'] = block if block else ''
return result
def listFileBlocks(self, dataset, onlyClosedBlocks=False, blockName=None):
"""
_listFileBlocks_
Retrieve a list of fileblock names for a dataset
"""
self.checkDatasetPath(dataset)
args = {'dataset': dataset, 'detail': False}
if blockName:
args['block_name'] = blockName
if onlyClosedBlocks:
args['detail'] = True
try:
blocks = self.dbs.listBlocks(**args)
except dbsClientException as ex:
msg = "Error in DBSReader.listFileBlocks(%s)\n" % dataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if onlyClosedBlocks:
result = [
x['block_name'] for x in blocks
if str(x['open_for_writing']) != "1"
]
else:
result = [x['block_name'] for x in blocks]
return result
def listOpenFileBlocks(self, dataset):
"""
_listOpenFileBlocks_
Retrieve a list of open fileblock names for a dataset
"""
self.checkDatasetPath(dataset)
try:
blocks = self.dbs.listBlocks(dataset=dataset, detail=True)
except dbsClientException as ex:
msg = "Error in DBSReader.listFileBlocks(%s)\n" % dataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
result = [
x['block_name'] for x in blocks
if str(x['open_for_writing']) == "1"
]
return result
def blockExists(self, fileBlockName):
"""
_blockExists_
Check to see if block with name provided exists in the DBS
Instance.
Return True if exists, False if not
"""
self.checkBlockName(fileBlockName)
try:
blocks = self.dbs.listBlocks(block_name=fileBlockName)
except Exception as ex:
msg = "Error in "
msg += "DBSReader.blockExists(%s)\n" % fileBlockName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if len(blocks) == 0:
return False
return True
def listFilesInBlock(self, fileBlockName, lumis=True, validFileOnly=1):
"""
_listFilesInBlock_
Get a list of files in the named fileblock
TODO: lumis can be false when lumi splitting is not required
However WMBSHelper expect file['LumiList'] to get the run number
so for now it will be always true.
We need to clean code up when dbs2 is completely deprecated.
calling lumis for run number is expensive.
"""
if not self.blockExists(fileBlockName):
msg = "DBSReader.listFilesInBlock(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
try:
files = self.dbs.listFileArray(block_name=fileBlockName,
validFileOnly=validFileOnly,
detail=True)
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listFilesInBlock(%s)\n" % fileBlockName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if lumis:
lumiDict = self._getLumiList(blockName=fileBlockName,
validFileOnly=validFileOnly)
result = []
for fileInfo in files:
if lumis:
fileInfo["LumiList"] = lumiDict[fileInfo['logical_file_name']]
result.append(remapDBS3Keys(fileInfo, stringify=True))
return result
def listFilesInBlockWithParents(self,
fileBlockName,
lumis=True,
validFileOnly=1):
"""
_listFilesInBlockWithParents_
Get a list of files in the named fileblock including
the parents of that file.
TODO: lumis can be false when lumi splitting is not required
However WMBSHelper expect file['LumiList'] to get the run number
so for now it will be always true.
"""
if not self.blockExists(fileBlockName):
msg = "DBSReader.listFilesInBlockWithParents(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
try:
# TODO: shoud we get only valid block for this?
files = self.dbs.listFileParents(block_name=fileBlockName)
fileDetails = self.listFilesInBlock(fileBlockName, lumis,
validFileOnly)
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listFilesInBlockWithParents(%s)\n" % (
fileBlockName, )
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
childByParents = defaultdict(list)
for f in files:
# Probably a child can have more than 1 parent file
for fp in f['parent_logical_file_name']:
childByParents[fp].append(f['logical_file_name'])
parentsLFNs = list(childByParents)
if len(parentsLFNs) == 0:
msg = "Error in "
msg += "DBSReader.listFilesInBlockWithParents(%s)\n There is no parents files" % (
fileBlockName)
raise DBSReaderError(msg)
parentFilesDetail = []
# TODO: slicing parentLFNs util DBS api is handling that.
# Remove slicing if DBS api handles
for pLFNs in grouper(parentsLFNs, 50):
parentFilesDetail.extend(
self.dbs.listFileArray(logical_file_name=pLFNs, detail=True))
if lumis:
parentLumis = self._getLumiList(lfns=parentsLFNs)
parentsByLFN = defaultdict(list)
for pf in parentFilesDetail:
parentLFN = pf['logical_file_name']
dbsFile = remapDBS3Keys(pf, stringify=True)
if lumis:
dbsFile["LumiList"] = parentLumis[parentLFN]
for childLFN in childByParents[parentLFN]:
parentsByLFN[childLFN].append(dbsFile)
for fileInfo in fileDetails:
fileInfo["ParentList"] = parentsByLFN[
fileInfo['logical_file_name']]
return fileDetails
def lfnsInBlock(self, fileBlockName):
"""
_lfnsInBlock_
LFN list only for block, details = False => faster query
"""
if not self.blockExists(fileBlockName):
msg = "DBSReader.lfnsInBlock(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
try:
lfns = self.dbs.listFileArray(block_name=fileBlockName,
validFileOnly=1,
detail=False)
return lfns
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listFilesInBlock(%s)\n" % fileBlockName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
def listFileBlockLocation(self, fileBlockNames):
"""
_listFileBlockLocation_
Get origin_site_name of a block
"""
singleBlockName = None
if isinstance(fileBlockNames, (str, bytes)):
singleBlockName = fileBlockNames
fileBlockNames = [fileBlockNames]
for block in fileBlockNames:
self.checkBlockName(block)
locations = {}
node_filter = set(['UNKNOWN', None])
blocksInfo = {}
try:
for block in fileBlockNames:
blocksInfo.setdefault(block, [])
# there should be only one element with a single origin site string ...
for blockInfo in self.dbs.listBlockOrigin(block_name=block):
blocksInfo[block].append(blockInfo['origin_site_name'])
except dbsClientException as ex:
msg = "Error in DBS3Reader: self.dbs.listBlockOrigin(block_name=%s)\n" % fileBlockNames
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
for block in fileBlockNames:
valid_nodes = set(blocksInfo.get(block, [])) - node_filter
locations[block] = list(valid_nodes)
# returning single list if a single block is passed
if singleBlockName:
return locations[singleBlockName]
return locations
def getFileBlock(self, fileBlockName):
"""
Retrieve a list of files in the block; a flag whether the
block is still open or not; and it used to resolve the block
location via PhEDEx.
:return: a dictionary in the format of:
{"PhEDExNodeNames" : [],
"Files" : { LFN : Events },
"IsOpen" : True|False}
"""
result = {
"PhEDExNodeNames": [], # FIXME: we better get rid of this line!
"Files": self.listFilesInBlock(fileBlockName),
"IsOpen": self.blockIsOpen(fileBlockName)
}
return result
def getFileBlockWithParents(self, fileBlockName):
"""
Retrieve a list of parent files in the block; a flag whether the
block is still open or not; and it used to resolve the block
location via PhEDEx.
:return: a dictionary in the format of:
{"PhEDExNodeNames" : [],
"Files" : { LFN : Events },
"IsOpen" : True|False}
"""
fileBlockName = decodeBytesToUnicode(fileBlockName)
if not self.blockExists(fileBlockName):
msg = "DBSReader.getFileBlockWithParents(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
result = {
"PhEDExNodeNames": [], # FIXME: we better get rid of this line!
"Files": self.listFilesInBlockWithParents(fileBlockName),
"IsOpen": self.blockIsOpen(fileBlockName)
}
return result
def listBlockParents(self, blockName):
"""
Return a list of parent blocks for a given child block name
"""
# FIXME: note the different returned data structure
result = []
self.checkBlockName(blockName)
blocks = self.dbs.listBlockParents(block_name=blockName)
result = [block['parent_block_name'] for block in blocks]
return result
def blockIsOpen(self, blockName):
"""
_blockIsOpen_
Return True if named block is open, false if not, or if block
doenst exist
"""
self.checkBlockName(blockName)
blockInstance = self.dbs.listBlocks(block_name=blockName, detail=True)
if len(blockInstance) == 0:
return False
blockInstance = blockInstance[0]
isOpen = blockInstance.get('open_for_writing', 1)
if isOpen == 0:
return False
return True
def blockToDatasetPath(self, blockName):
"""
_blockToDatasetPath_
Given a block name, get the dataset Path associated with that
Block.
Returns the dataset path, or None if not found
"""
self.checkBlockName(blockName)
try:
blocks = self.dbs.listBlocks(block_name=blockName, detail=True)
except Exception as ex:
msg = "Error in "
msg += "DBSReader.blockToDatasetPath(%s)\n" % blockName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if blocks == []:
return None
pathname = blocks[-1].get('dataset', None)
return pathname
def listDatasetLocation(self, datasetName):
"""
_listDatasetLocation_
List the origin SEs where there is at least a block of the given
dataset.
"""
self.checkDatasetPath(datasetName)
locations = set()
try:
blocksInfo = self.dbs.listBlockOrigin(dataset=datasetName)
except dbsClientException as ex:
msg = "Error in DBSReader: dbsApi.listBlocks(dataset=%s)\n" % datasetName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if not blocksInfo: # no data location from dbs
return list()
for blockInfo in blocksInfo:
locations.update(blockInfo['origin_site_name'])
locations.difference_update(
['UNKNOWN', None]) # remove entry when SE name is 'UNKNOWN'
return list(locations)
def checkDatasetPath(self, pathName):
"""
_checkDatasetPath_
"""
if pathName in ("", None):
raise DBSReaderError("Invalid Dataset Path name: => %s <=" %
pathName)
else:
try:
result = self.dbs.listDatasets(dataset=pathName,
dataset_access_type='*')
if len(result) == 0:
raise DBSReaderError("Dataset %s doesn't exist in DBS %s" %
(pathName, self.dbsURL))
except (dbsClientException, HTTPError) as ex:
msg = "Error in "
msg += "DBSReader.checkDatasetPath(%s)\n" % pathName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
return
def checkBlockName(self, blockName):
"""
_checkBlockName_
"""
if blockName in ("", "*", None):
raise DBSReaderError("Invalid Block name: => %s <=" % blockName)
def getFileListByDataset(self, dataset, validFileOnly=1, detail=True):
"""
_getFileListByDataset_
Given a dataset, retrieves all blocks, lfns and number of events (among other
not really important info).
Returns a list of dict.
"""
try:
fileList = self.dbs.listFileArray(dataset=dataset,
validFileOnly=validFileOnly,
detail=detail)
return fileList
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.getFileListByDataset(%s)\n" % dataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
def listDatasetParents(self, childDataset):
"""
list the the parents dataset path given childDataset
"""
try:
parentList = self.dbs.listDatasetParents(dataset=childDataset)
return parentList
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listDatasetParents(%s)\n" % childDataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
# def getListFilesByLumiAndDataset(self, dataset, files):
# "Unsing pycurl to get all the child parents pair for given dataset"
#
# urls = ['%s/data/dbs/fileparentbylumis?block_name=%s' % (
# self.dbsURL, b["block_name"]) for b in self.dbs.listBlocks(dataset=dataset)]
#
# data = multi_getdata(urls, ckey(), cert())
# rdict = {}
# for row in data:
# try:
# data = json.loads(row['data'])
# rdict[req] = data['result'][0] # we get back {'result': [workflow]} dict
# except Exception as exp:
# print("ERROR: fail to load data as json record, error=%s" % str(exp))
# print(row)
# return rdict
def getParentFilesGivenParentDataset(self, parentDataset, childLFNs):
"""
returns parent files for given childLFN when DBS doesn't have direct parent child relationship in DB
Only use this for finding missing parents
:param parentDataset: parent dataset for childLFN
:param childLFN: a file in child dataset
:return: set of parent files for childLFN
"""
fInfo = self.dbs.listFileLumiArray(logical_file_name=childLFNs)
parentFiles = defaultdict(set)
for f in fInfo:
pFileList = self.dbs.listFiles(dataset=parentDataset,
run_num=f['run_num'],
lumi_list=f['lumi_section_num'])
pFiles = set([x['logical_file_name'] for x in pFileList])
parentFiles[f['logical_file_name']] = parentFiles[
f['logical_file_name']].union(pFiles)
return parentFiles
def getParentFilesByLumi(self, childLFN):
"""
get the parent file's lfns by lumi (This might not be the actual parentage relations in DBS just parentage by Lumis).
use for only specific lfn for validating purpose, for the parentage fix use findAndInsertMissingParentage
:param childLFN:
:return: list of dictionary with parent files for given child LFN and parent dataset
[{"ParentDataset": /abc/bad/ddd, "ParentFiles": [alf, baf, ...]]
"""
childDatasets = self.dbs.listDatasets(logical_file_name=childLFN)
result = []
for i in childDatasets:
parents = self.dbs.listDatasetParents(dataset=i["dataset"])
for parent in parents:
parentFiles = self.getParentFilesGivenParentDataset(
parent['parent_dataset'], childLFN)
result.append({
"ParentDataset": parent['parent_dataset'],
"ParentFiles": list(parentFiles)
})
return result
def insertFileParents(self, childBlockName, childParentsIDPairs):
"""
:param childBlockName: child block name
:param childParentsIDPairs: list of list child and parent file ids, i.e. [[1,2], [3,4]...]
dbs validate child ids from the childBlockName
:return: None
"""
return self.dbs.insertFileParents({
"block_name":
childBlockName,
"child_parent_id_list":
childParentsIDPairs
})
def findAndInsertMissingParentage(self,
childBlockName,
parentData,
insertFlag=True):
"""
:param childBlockName: child block name
:param parentData: a dictionary with complete parent dataset file/run/lumi information
:param insertFlag: boolean to allow parentage insertion into DBS or not
:return: number of file parents pair inserted
"""
# in the format of: {'fileid': [[run_num1, lumi1], [run_num1, lumi2], etc]
# e.g. {'554307997': [[1, 557179], [1, 557178], [1, 557181],
childBlockData = self.dbs.listBlockTrio(block_name=childBlockName)
# runs the actual mapping logic, like {"child_id": ["parent_id", "parent_id2", ...], etc
mapChildParent = {}
# there should be only 1 item, but we better be safe
for item in childBlockData:
for childFileID in item:
for runLumiPair in item[childFileID]:
frozenKey = frozenset(runLumiPair)
parentId = parentData.get(frozenKey)
if parentId is None:
msg = "Child file id: %s, with run/lumi: %s, has no match in the parent dataset"
self.logger.warning(msg, childFileID, frozenKey)
continue
mapChildParent.setdefault(childFileID, set())
mapChildParent[childFileID].add(parentId)
if insertFlag and mapChildParent:
# convert dictionary to list of unique childID, parentID tuples
listChildParent = []
for childID in mapChildParent:
for parentID in mapChildParent[childID]:
listChildParent.append([int(childID), int(parentID)])
self.dbs.insertFileParents({
"block_name": childBlockName,
"child_parent_id_list": listChildParent
})
return len(mapChildParent)
def listBlocksWithNoParents(self, childDataset):
"""
:param childDataset: child dataset for
:return: set of child blocks with no parentBlock
"""
allBlocks = self.dbs.listBlocks(dataset=childDataset)
blockNames = []
for block in allBlocks:
blockNames.append(block['block_name'])
parentBlocks = self.dbs.listBlockParents(block_name=blockNames)
cblock = set()
for pblock in parentBlocks:
cblock.add(pblock['this_block_name'])
noParentBlocks = set(blockNames) - cblock
return noParentBlocks
def listFilesWithNoParents(self, childBlockName):
"""
:param childBlockName:
:return:
"""
allFiles = self.dbs.listFiles(block_name=childBlockName)
parentFiles = self.dbs.listFileParents(block_name=childBlockName)
allFileNames = set()
for fInfo in allFiles:
allFileNames.add(fInfo['logical_file_name'])
cfile = set()
for pFile in parentFiles:
cfile.add(pFile['logical_file_name'])
noParentFiles = allFileNames - cfile
return list(noParentFiles)
def fixMissingParentageDatasets(self, childDataset, insertFlag=True):
"""
:param childDataset: child dataset need to set the parentage correctly.
:return: blocks which failed to insert parentage. for retry
"""
pDatasets = self.listDatasetParents(childDataset)
self.logger.info("Parent datasets for %s are: %s", childDataset,
pDatasets)
# print("parent datasets %s\n" % pDatasets)
# pDatasets format is
# [{'this_dataset': '/SingleMuon/Run2016D-03Feb2017-v1/MINIAOD', 'parent_dataset_id': 13265209, 'parent_dataset': '/SingleMuon/Run2016D-23Sep2016-v1/AOD'}]
if not pDatasets:
self.logger.warning("No parent dataset found for child dataset %s",
childDataset)
return {}
parentFullInfo = self.getParentDatasetTrio(childDataset)
blocks = self.listBlocksWithNoParents(childDataset)
failedBlocks = []
self.logger.info("Found %d blocks without parentage information",
len(blocks))
for blockName in blocks:
try:
self.logger.info("Fixing parentage for block: %s", blockName)
numFiles = self.findAndInsertMissingParentage(
blockName, parentFullInfo, insertFlag=insertFlag)
self.logger.debug("%s file parentage added for block %s",
numFiles, blockName)
except Exception as ex:
self.logger.exception("Parentage updated failed for block %s",
blockName)
failedBlocks.append(blockName)
return failedBlocks
def getParentDatasetTrio(self, childDataset):
"""
Provided a dataset name, return all the parent dataset information, such as:
- file ids, run number and lumi section
NOTE: This API is meant to be used by the StepChainParentage thread only!!!
:param childDataset: name of the child dataset
:return: a dictionary where the key is a set of run/lumi, its value is the fileid
"""
# this will return data in the format of:
# {'554307997': [[1, 557179], [1, 557178],...
# such that: key is file id, in each list is [run_number, lumi_section_numer].
parentFullInfo = self.dbs.listParentDSTrio(dataset=childDataset)
# runs the actual mapping logic, like {"child_id": ["parent_id", "parent_id2", ...], etc
parentFrozenData = {}
for item in parentFullInfo:
for fileId in item:
for runLumiPair in item[fileId]:
frozenKey = frozenset(runLumiPair)
parentFrozenData[frozenKey] = fileId
return parentFrozenData
class DBS3Reader(object):
"""
_DBSReader_
General API for reading data from DBS
"""
# cache all the datatiers known by DBS
_datatiers = {}
def __init__(self, url, logger=None, **contact):
# instantiate dbs api object
try:
self.dbsURL = url
self.dbs = DbsApi(url, **contact)
self.logger = logger or logging.getLogger(self.__class__.__name__)
except dbsClientException as ex:
msg = "Error in DBSReader with DbsApi\n"
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
# connection to PhEDEx (Use default endpoint url)
self.phedex = PhEDEx(responseType="json", dbsUrl=self.dbsURL)
def _getLumiList(self, blockName=None, lfns=None, validFileOnly=1):
"""
currently only take one lfn but dbs api need be updated
"""
try:
if blockName:
lumiLists = self.dbs.listFileLumis(block_name=blockName, validFileOnly=validFileOnly)
elif lfns:
lumiLists = []
for slfn in grouper(lfns, 50):
lumiLists.extend(self.dbs.listFileLumiArray(logical_file_name=slfn))
else:
# shouldn't call this with both blockName and lfns empty
# but still returns empty dict for that case
return {}
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listFileLumiArray(%s)\n" % lfns
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
lumiDict = {}
for lumisItem in lumiLists:
lumiDict.setdefault(lumisItem['logical_file_name'], [])
item = {}
item["RunNumber"] = lumisItem['run_num']
item['LumiSectionNumber'] = lumisItem['lumi_section_num']
if lumisItem.get('event_count', None) is not None:
item['EventCount'] = lumisItem['event_count']
lumiDict[lumisItem['logical_file_name']].append(item)
# TODO: add key for lumi and event pair.
return lumiDict
def checkDBSServer(self):
"""
check whether dbs server is up and running
returns {"dbs_instance": "prod/global", "dbs_version": "3.3.144"}
"""
try:
return self.dbs.serverinfo()
except dbsClientException as ex:
msg = "Error in "
msg += "DBS server is not up: %s" % self.dbsURL
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
def listPrimaryDatasets(self, match='*'):
"""
_listPrimaryDatasets_
return a list of primary datasets, The full dataset name must be provided
pattern based mathcing is no longer supported.
If no expression is provided, all datasets are returned
"""
try:
result = self.dbs.listPrimaryDatasets(primary_ds_name=match)
except dbsClientException as ex:
msg = "Error in DBSReader.listPrimaryDataset(%s)\n" % match
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
result = [x['primary_ds_name'] for x in result]
return result
def matchProcessedDatasets(self, primary, tier, process):
"""
_matchProcessedDatasets_
return a list of Processed datasets
"""
result = []
try:
datasets = self.dbs.listDatasets(primary_ds_name=primary, data_tier_name=tier, detail=True)
except dbsClientException as ex:
msg = "Error in DBSReader.listProcessedDatasets(%s)\n" % primary
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
for dataset in datasets:
dataset = remapDBS3Keys(dataset, processed_ds_name='Name')
dataset['PathList'] = [dataset['dataset']]
if dataset['Name'] == process:
result.append(dataset)
return result
def listRuns(self, dataset=None, block=None):
"""
it gets list of DbsRun object but for our purpose
only list of number is collected.
DbsRun (RunNumber,
NumberOfEvents,
NumberOfLumiSections,
TotalLuminosity,
StoreNumber,
StartOfRungetLong,
EndOfRun,
CreationDate,
CreatedBy,
LastModificationDate,
LastModifiedBy
)
"""
runs = []
try:
if block:
results = self.dbs.listRuns(block_name=block)
else:
results = self.dbs.listRuns(dataset=dataset)
except dbsClientException as ex:
msg = "Error in DBSReader.listRuns(%s, %s)\n" % (dataset, block)
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
for x in results:
runs.extend(x['run_num'])
return runs
def listRunLumis(self, dataset=None, block=None):
"""
It gets a list of DBSRun objects and returns the number of lumisections per run
DbsRun (RunNumber,
NumberOfEvents,
NumberOfLumiSections,
TotalLuminosity,
StoreNumber,
StartOfRungetLong,
EndOfRun,
CreationDate,
CreatedBy,
LastModificationDate,
LastModifiedBy
)
"""
# Pointless code in python3
if isinstance(block, str):
block = unicode(block)
if isinstance(dataset, str):
dataset = unicode(dataset)
try:
if block:
results = self.dbs.listRuns(block_name=block)
else:
results = self.dbs.listRuns(dataset=dataset)
except dbsClientException as ex:
msg = "Error in DBSReader.listRuns(%s, %s)\n" % (dataset, block)
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
# send runDict format as result, this format is for sync with dbs2 call
# which has {run_number: num_lumis} but dbs3 call doesn't return num Lumis
# So it returns {run_number: None}
# TODO: After DBS2 is completely removed change the return format more sensible one
runDict = {}
for x in results:
for runNumber in x["run_num"]:
runDict[runNumber] = None
return runDict
def listProcessedDatasets(self, primary, dataTier='*'):
"""
_listProcessedDatasets_
return a list of Processed datasets for the primary and optional
data tier value
"""
try:
result = self.dbs.listDatasets(primary_ds_name=primary, data_tier_name=dataTier)
except dbsClientException as ex:
msg = "Error in DBSReader.listProcessedDatasets(%s)\n" % primary
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
result = [x['dataset'].split('/')[2] for x in result]
return result
def listDatasetFiles(self, datasetPath):
"""
_listDatasetFiles_
Get list of files for dataset
"""
return [x['logical_file_name'] for x in self.dbs.listFileArray(dataset=datasetPath)]
@staticmethod
def listDatatiers(dbsUrl=None):
"""
_listDatatiers_
Get a list of datatiers known by DBS.
"""
if dbsUrl is None:
msg = "Error in DBSReader.listDatatiers(). DBS Url not set."
raise DBSReaderError(msg)
timenow = int(time.time())
if DBS3Reader._datatiers and timenow - 7200 < DBS3Reader._datatiers['ts']:
return DBS3Reader._datatiers['tiers']
try:
DBS3Reader._setDatatiersCache(timenow, dbsUrl)
except Exception as ex:
if not DBS3Reader._datatiers:
msg = "Error in DBSReader.listDatatiers\n%s" % formatEx3(ex)
raise DBSReaderError(msg)
return DBS3Reader._datatiers['tiers']
@staticmethod
def _setDatatiersCache(ts, dbsUrl):
"""
Set a timestamp and update the list of datatiers cached in
the class property
"""
dbs = DbsApi(dbsUrl)
DBS3Reader._datatiers['ts'] = ts
DBS3Reader._datatiers['tiers'] = [tier['data_tier_name'] for tier in dbs.listDataTiers()]
return
def listDatasetFileDetails(self, datasetPath, getParents=False, getLumis=True, validFileOnly=1):
"""
TODO: This is completely wrong need to be redone. or be removed - getting dataset altogether
might be to costly
_listDatasetFileDetails_
Get list of lumis, events, and parents for each file in a dataset
Return a dict where the keys are the files, and for each file we have something like:
{ 'NumberOfEvents': 545,
'BlockName': '/HighPileUp/Run2011A-v1/RAW#dd6e0796-cbcc-11e0-80a9-003048caaace',
'Lumis': {173658: [8, 12, 9, 14, 19, 109, 105]},
'Parents': [],
'Checksum': '22218315',
'Adler32': 'a41a1446',
'FileSize': 286021145,
'ValidFile': 1
}
"""
fileDetails = self.getFileListByDataset(dataset=datasetPath, validFileOnly=validFileOnly, detail=True)
blocks = set() # the set of blocks of the dataset
# Iterate over the files and prepare the set of blocks and a dict where the keys are the files
files = {}
for f in fileDetails:
blocks.add(f['block_name'])
files[f['logical_file_name']] = remapDBS3Keys(f, stringify=True)
files[f['logical_file_name']]['ValidFile'] = f['is_file_valid']
files[f['logical_file_name']]['Lumis'] = {}
files[f['logical_file_name']]['Parents'] = []
# Iterate over the blocks and get parents and lumis
for blockName in blocks:
# get the parents
if getParents:
parents = self.dbs.listFileParents(block_name=blockName)
for p in parents:
if p['logical_file_name'] in files: # invalid files are not there if validFileOnly=1
files[p['logical_file_name']]['Parents'].extend(p['parent_logical_file_name'])
if getLumis:
# get the lumis
file_lumis = self.dbs.listFileLumis(block_name=blockName)
for f in file_lumis:
if f['logical_file_name'] in files: # invalid files are not there if validFileOnly=1
if f['run_num'] in files[f['logical_file_name']]['Lumis']:
files[f['logical_file_name']]['Lumis'][f['run_num']].extend(f['lumi_section_num'])
else:
files[f['logical_file_name']]['Lumis'][f['run_num']] = f['lumi_section_num']
return files
def crossCheck(self, datasetPath, *lfns):
"""
_crossCheck_
For the dataset provided, check that the lfns listed all exist
in the dataset.
Return the list of lfns that are in the dataset
"""
allLfns = self.dbs.listFileArray(dataset=datasetPath, validFileOnly=1, detail=False)
setOfAllLfns = set(allLfns)
setOfKnownLfns = set(lfns)
return list(setOfAllLfns.intersection(setOfKnownLfns))
def crossCheckMissing(self, datasetPath, *lfns):
"""
_crossCheckMissing_
As cross check, but return value is a list of files that
are *not* known by DBS
"""
allLfns = self.dbs.listFileArray(dataset=datasetPath, validFileOnly=1, detail=False)
setOfAllLfns = set(allLfns)
setOfKnownLfns = set(lfns)
knownFiles = setOfAllLfns.intersection(setOfKnownLfns)
unknownFiles = setOfKnownLfns.difference(knownFiles)
return list(unknownFiles)
def getDBSSummaryInfo(self, dataset=None, block=None):
"""
Get dataset summary includes # of files, events, blocks and total size
"""
if dataset:
self.checkDatasetPath(dataset)
try:
if block:
summary = self.dbs.listFileSummaries(block_name=block, validFileOnly=1)
else:
summary = self.dbs.listFileSummaries(dataset=dataset, validFileOnly=1)
except Exception as ex:
msg = "Error in DBSReader.getDBSSummaryInfo(%s, %s)\n" % (dataset, block)
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if not summary: # missing data or all files invalid
return {}
result = remapDBS3Keys(summary[0], stringify=True)
result['path'] = dataset if dataset else ''
result['block'] = block if block else ''
return result
def getFileBlocksInfo(self, dataset, onlyClosedBlocks=False,
blockName=None, locations=True):
"""
"""
self.checkDatasetPath(dataset)
args = {'dataset': dataset, 'detail': True}
if blockName:
args['block_name'] = blockName
try:
blocks = self.dbs.listBlocks(**args)
except Exception as ex:
msg = "Error in DBSReader.getFileBlocksInfo(%s)\n" % dataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
blocks = [remapDBS3Keys(block, stringify=True, block_name='Name') for block in blocks]
# only raise if blockName not specified - mimic dbs2 error handling
if not blocks and not blockName:
msg = "DBSReader.getFileBlocksInfo(%s, %s): No matching data"
raise DBSReaderError(msg % (dataset, blockName))
if locations:
for block in blocks:
block['PhEDExNodeList'] = [{'Name': x} for x in self.listFileBlockLocation(block['Name'])]
if onlyClosedBlocks:
return [x for x in blocks if str(x['OpenForWriting']) != "1"]
return blocks
def listFileBlocks(self, dataset, onlyClosedBlocks=False, blockName=None):
"""
_listFileBlocks_
Retrieve a list of fileblock names for a dataset
"""
self.checkDatasetPath(dataset)
args = {'dataset': dataset, 'detail': False}
if blockName:
args['block_name'] = blockName
if onlyClosedBlocks:
args['detail'] = True
try:
blocks = self.dbs.listBlocks(**args)
except dbsClientException as ex:
msg = "Error in DBSReader.listFileBlocks(%s)\n" % dataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if onlyClosedBlocks:
result = [x['block_name'] for x in blocks if str(x['open_for_writing']) != "1"]
else:
result = [x['block_name'] for x in blocks]
return result
def listOpenFileBlocks(self, dataset):
"""
_listOpenFileBlocks_
Retrieve a list of open fileblock names for a dataset
"""
self.checkDatasetPath(dataset)
try:
blocks = self.dbs.listBlocks(dataset=dataset, detail=True)
except dbsClientException as ex:
msg = "Error in DBSReader.listFileBlocks(%s)\n" % dataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
result = [x['block_name'] for x in blocks if str(x['open_for_writing']) == "1"]
return result
def blockExists(self, fileBlockName):
"""
_blockExists_
Check to see if block with name provided exists in the DBS
Instance.
Return True if exists, False if not
"""
self.checkBlockName(fileBlockName)
try:
blocks = self.dbs.listBlocks(block_name=fileBlockName)
except Exception as ex:
msg = "Error in "
msg += "DBSReader.blockExists(%s)\n" % fileBlockName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if len(blocks) == 0:
return False
return True
def listFilesInBlock(self, fileBlockName, lumis=True, validFileOnly=1):
"""
_listFilesInBlock_
Get a list of files in the named fileblock
TODO: lumis can be false when lumi splitting is not required
However WMBSHelper expect file['LumiList'] to get the run number
so for now it will be always true.
We need to clean code up when dbs2 is completely deprecated.
calling lumis for run number is expensive.
"""
if not self.blockExists(fileBlockName):
msg = "DBSReader.listFilesInBlock(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
try:
files = self.dbs.listFileArray(block_name=fileBlockName, validFileOnly=validFileOnly, detail=True)
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listFilesInBlock(%s)\n" % fileBlockName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if lumis:
lumiDict = self._getLumiList(blockName=fileBlockName, validFileOnly=validFileOnly)
result = []
for fileInfo in files:
if lumis:
fileInfo["LumiList"] = lumiDict[fileInfo['logical_file_name']]
result.append(remapDBS3Keys(fileInfo, stringify=True))
return result
def listFilesInBlockWithParents(self, fileBlockName, lumis=True, validFileOnly=1):
"""
_listFilesInBlockWithParents_
Get a list of files in the named fileblock including
the parents of that file.
TODO: lumis can be false when lumi splitting is not required
However WMBSHelper expect file['LumiList'] to get the run number
so for now it will be always true.
"""
if not self.blockExists(fileBlockName):
msg = "DBSReader.listFilesInBlockWithParents(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
try:
# TODO: shoud we get only valid block for this?
files = self.dbs.listFileParents(block_name=fileBlockName)
fileDetails = self.listFilesInBlock(fileBlockName, lumis, validFileOnly)
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listFilesInBlockWithParents(%s)\n" % (
fileBlockName,)
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
childByParents = defaultdict(list)
for f in files:
# Probably a child can have more than 1 parent file
for fp in f['parent_logical_file_name']:
childByParents[fp].append(f['logical_file_name'])
parentsLFNs = childByParents.keys()
if len(parentsLFNs) == 0:
msg = "Error in "
msg += "DBSReader.listFilesInBlockWithParents(%s)\n There is no parents files" % (
fileBlockName)
raise DBSReaderError(msg)
parentFilesDetail = []
# TODO: slicing parentLFNs util DBS api is handling that.
# Remove slicing if DBS api handles
for pLFNs in grouper(parentsLFNs, 50):
parentFilesDetail.extend(self.dbs.listFileArray(logical_file_name=pLFNs, detail=True))
if lumis:
parentLumis = self._getLumiList(lfns=parentsLFNs)
parentsByLFN = defaultdict(list)
for pf in parentFilesDetail:
parentLFN = pf['logical_file_name']
dbsFile = remapDBS3Keys(pf, stringify=True)
if lumis:
dbsFile["LumiList"] = parentLumis[parentLFN]
for childLFN in childByParents[parentLFN]:
parentsByLFN[childLFN].append(dbsFile)
for fileInfo in fileDetails:
fileInfo["ParentList"] = parentsByLFN[fileInfo['logical_file_name']]
return fileDetails
def lfnsInBlock(self, fileBlockName):
"""
_lfnsInBlock_
LFN list only for block, details = False => faster query
"""
if not self.blockExists(fileBlockName):
msg = "DBSReader.lfnsInBlock(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
try:
lfns = self.dbs.listFileArray(block_name=fileBlockName, validFileOnly=1, detail=False)
return lfns
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listFilesInBlock(%s)\n" % fileBlockName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
def listFileBlockLocation(self, fileBlockNames, dbsOnly=False):
"""
_listFileBlockLocation_
Get origin_site_name of a block
"""
singleBlockName = None
if isinstance(fileBlockNames, basestring):
singleBlockName = fileBlockNames
fileBlockNames = [fileBlockNames]
for block in fileBlockNames:
self.checkBlockName(block)
locations = {}
node_filter = set(['UNKNOWN', None])
if dbsOnly:
blocksInfo = {}
try:
for block in fileBlockNames:
blocksInfo.setdefault(block, [])
# there should be only one element with a single origin site string ...
for blockInfo in self.dbs.listBlockOrigin(block_name=block):
blocksInfo[block].append(blockInfo['origin_site_name'])
except dbsClientException as ex:
msg = "Error in DBS3Reader: self.dbs.listBlockOrigin(block_name=%s)\n" % fileBlockNames
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
else:
try:
blocksInfo = self.phedex.getReplicaPhEDExNodesForBlocks(block=fileBlockNames, complete='y')
except Exception as ex:
msg = "Error while getting block location from PhEDEx for block_name=%s)\n" % fileBlockNames
msg += "%s\n" % str(ex)
raise Exception(msg)
for block in fileBlockNames:
valid_nodes = set(blocksInfo.get(block, [])) - node_filter
locations[block] = list(valid_nodes)
# returning single list if a single block is passed
if singleBlockName:
return locations[singleBlockName]
return locations
def getFileBlock(self, fileBlockName, dbsOnly=False):
"""
_getFileBlock_
dbsOnly flag is mostly meant for StoreResults, since there is no
data in TMDB.
return a dictionary:
{ blockName: {
"PhEDExNodeNames" : [<pnn list>],
"Files" : { LFN : Events },
}
}
"""
# Pointless code in python3
if isinstance(fileBlockName, str):
fileBlockName = unicode(fileBlockName)
if not self.blockExists(fileBlockName):
msg = "DBSReader.getFileBlock(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
result = {fileBlockName: {
"PhEDExNodeNames": self.listFileBlockLocation(fileBlockName, dbsOnly),
"Files": self.listFilesInBlock(fileBlockName),
"IsOpen": self.blockIsOpen(fileBlockName)
}
}
return result
def getFileBlockWithParents(self, fileBlockName):
"""
_getFileBlockWithParents_
return a dictionary:
{ blockName: {
"PhEDExNodeNames" : [<pnn list>],
"Files" : dictionaries representing each file
}
}
files
"""
if isinstance(fileBlockName, str):
fileBlockName = unicode(fileBlockName)
if not self.blockExists(fileBlockName):
msg = "DBSReader.getFileBlockWithParents(%s): No matching data"
raise DBSReaderError(msg % fileBlockName)
result = {fileBlockName: {
"PhEDExNodeNames": self.listFileBlockLocation(fileBlockName),
"Files": self.listFilesInBlockWithParents(fileBlockName),
"IsOpen": self.blockIsOpen(fileBlockName)
}
}
return result
def getFiles(self, dataset, onlyClosedBlocks=False):
"""
_getFiles_
Returns a dictionary of block names for the dataset where
each block constists of a dictionary containing the PhEDExNodeNames
for that block and the files in that block by LFN mapped to NEvents
"""
result = {}
blocks = self.listFileBlocks(dataset, onlyClosedBlocks)
for x in blocks:
result.update(self.getFileBlock(x))
return result
def listBlockParents(self, blockName):
"""Get parent blocks for block"""
result = []
self.checkBlockName(blockName)
blocks = self.dbs.listBlockParents(block_name=blockName)
for block in blocks:
toreturn = {'Name': block['parent_block_name']}
toreturn['PhEDExNodeList'] = self.listFileBlockLocation(toreturn['Name'])
result.append(toreturn)
return result
def blockIsOpen(self, blockName):
"""
_blockIsOpen_
Return True if named block is open, false if not, or if block
doenst exist
"""
self.checkBlockName(blockName)
blockInstance = self.dbs.listBlocks(block_name=blockName, detail=True)
if len(blockInstance) == 0:
return False
blockInstance = blockInstance[0]
isOpen = blockInstance.get('open_for_writing', 1)
if isOpen == 0:
return False
return True
def blockToDatasetPath(self, blockName):
"""
_blockToDatasetPath_
Given a block name, get the dataset Path associated with that
Block.
Returns the dataset path, or None if not found
"""
self.checkBlockName(blockName)
try:
blocks = self.dbs.listBlocks(block_name=blockName, detail=True)
except Exception as ex:
msg = "Error in "
msg += "DBSReader.blockToDatasetPath(%s)\n" % blockName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if blocks == []:
return None
pathname = blocks[-1].get('dataset', None)
return pathname
def listDatasetLocation(self, datasetName, dbsOnly=False):
"""
_listDatasetLocation_
List the origin SEs where there is at least a block of the given
dataset.
"""
self.checkDatasetPath(datasetName)
locations = set()
if dbsOnly:
try:
blocksInfo = self.dbs.listBlockOrigin(dataset=datasetName)
except dbsClientException as ex:
msg = "Error in DBSReader: dbsApi.listBlocks(dataset=%s)\n" % datasetName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
if not blocksInfo: # no data location from dbs
return list()
for blockInfo in blocksInfo:
locations.update(blockInfo['origin_site_name'])
locations.difference_update(['UNKNOWN', None]) # remove entry when SE name is 'UNKNOWN'
else:
try:
blocksInfo = self.phedex.getReplicaPhEDExNodesForBlocks(dataset=[datasetName], complete='y')
except Exception as ex:
msg = "Error while getting block location from PhEDEx for dataset=%s)\n" % datasetName
msg += "%s\n" % str(ex)
raise Exception(msg)
if blocksInfo:
for blockSites in blocksInfo.values():
locations.update(blockSites)
return list(locations)
def checkDatasetPath(self, pathName):
"""
_checkDatasetPath_
"""
if pathName in ("", None):
raise DBSReaderError("Invalid Dataset Path name: => %s <=" % pathName)
else:
try:
result = self.dbs.listDatasets(dataset=pathName, dataset_access_type='*')
if len(result) == 0:
raise DBSReaderError("Dataset %s doesn't exist in DBS %s" % (pathName, self.dbsURL))
except (dbsClientException, HTTPError) as ex:
msg = "Error in "
msg += "DBSReader.checkDatasetPath(%s)\n" % pathName
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
return
def checkBlockName(self, blockName):
"""
_checkBlockName_
"""
if blockName in ("", "*", None):
raise DBSReaderError("Invalid Block name: => %s <=" % blockName)
def getFileListByDataset(self, dataset, validFileOnly=1, detail=True):
"""
_getFileListByDataset_
Given a dataset, retrieves all blocks, lfns and number of events (among other
not really important info).
Returns a list of dict.
"""
try:
fileList = self.dbs.listFileArray(dataset=dataset, validFileOnly=validFileOnly, detail=detail)
return fileList
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.getFileListByDataset(%s)\n" % dataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
def listDatasetParents(self, childDataset):
"""
list the the parents dataset path given childDataset
"""
try:
parentList = self.dbs.listDatasetParents(dataset=childDataset)
return parentList
except dbsClientException as ex:
msg = "Error in "
msg += "DBSReader.listDatasetParents(%s)\n" % childDataset
msg += "%s\n" % formatEx3(ex)
raise DBSReaderError(msg)
# def getListFilesByLumiAndDataset(self, dataset, files):
# "Unsing pycurl to get all the child parents pair for given dataset"
#
# urls = ['%s/data/dbs/fileparentbylumis?block_name=%s' % (
# self.dbsURL, b["block_name"]) for b in self.dbs.listBlocks(dataset=dataset)]
#
# data = multi_getdata(urls, ckey(), cert())
# rdict = {}
# for row in data:
# try:
# data = json.loads(row['data'])
# rdict[req] = data['result'][0] # we get back {'result': [workflow]} dict
# except Exception as exp:
# print("ERROR: fail to load data as json record, error=%s" % str(exp))
# print(row)
# return rdict
def getParentFilesGivenParentDataset(self, parentDataset, childLFNs):
"""
returns parent files for given childLFN when DBS doesn't have direct parent child relationship in DB
Only use this for finding missing parents
:param parentDataset: parent dataset for childLFN
:param childLFN: a file in child dataset
:return: set of parent files for childLFN
"""
fInfo = self.dbs.listFileLumiArray(logical_file_name=childLFNs)
parentFiles = defaultdict(set)
for f in fInfo:
pFileList = self.dbs.listFiles(dataset=parentDataset, run_num=f['run_num'], lumi_list=f['lumi_section_num'])
pFiles = set([x['logical_file_name'] for x in pFileList])
parentFiles[f['logical_file_name']] = parentFiles[f['logical_file_name']].union(pFiles)
return parentFiles
def getParentFilesByLumi(self, childLFN):
"""
get the parent file's lfns by lumi (This might not be the actual parentage relations in DBS just parentage by Lumis).
use for only specific lfn for validating purpose, for the parentage fix use findAndInsertMissingParentage
:param childLFN:
:return: list of dictionary with parent files for given child LFN and parent dataset
[{"ParentDataset": /abc/bad/ddd, "ParentFiles": [alf, baf, ...]]
"""
childDatasets = self.dbs.listDatasets(logical_file_name=childLFN)
result = []
for i in childDatasets:
parents = self.dbs.listDatasetParents(dataset=i["dataset"])
for parent in parents:
parentFiles = self.getParentFilesGivenParentDataset(parent['parent_dataset'], childLFN)
result.append({"ParentDataset": parent['parent_dataset'], "ParentFiles": list(parentFiles)})
return result
def listParentsByLumi(self, childBlockName, childLFNs=None):
"""
:param childBlockName: child block name
:param childLFNs: list of child lfns if it is not specified, all the file in the block will be used,
if specified, dbs validate child lfns from the childBlockName
:return: list of list with child and parent id pair. [[1,2], [3,4]...]
"""
childLFNs = childLFNs or []
return self.dbs.listFileParentsByLumi(block_name=childBlockName, logical_file_name=childLFNs)
def insertFileParents(self, childBlockName, childParentsIDPairs):
"""
:param childBlockName: child block name
:param childParentsIDPairs: list of list child and parent file ids, i.e. [[1,2], [3,4]...]
dbs validate child ids from the childBlockName
:return: None
"""
return self.dbs.insertFileParents({"block_name": childBlockName, "child_parent_id_list": childParentsIDPairs})
def findAndInsertMissingParentage(self, childBlockName, childLFNs=None, insertFlag=True):
"""
:param childBlockName: child block name
:param childLFNs: list of child lfns if it is not specified, all the file in the block will be used,
if specified, dbs validate child lfns from the childBlockName
:return: number of file parents pair inserted
"""
childLFNs = childLFNs or []
fileParents = self.dbs.listFileParentsByLumi(block_name=childBlockName, logical_file_name=childLFNs)
childParentsIDPairs = fileParents[0]["child_parent_id_list"]
if insertFlag:
self.dbs.insertFileParents({"block_name": childBlockName, "child_parent_id_list": childParentsIDPairs})
return len(childParentsIDPairs)
def listBlocksWithNoParents(self, childDataset):
"""
:param childDataset: child dataset for
:return: set of child blocks with no parentBlock
"""
allBlocks = self.dbs.listBlocks(dataset=childDataset)
blockNames = []
for block in allBlocks:
blockNames.append(block['block_name'])
parentBlocks = self.dbs.listBlockParents(block_name=blockNames)
cblock = set()
for pblock in parentBlocks:
cblock.add(pblock['this_block_name'])
noParentBlocks = set(blockNames) - cblock
return noParentBlocks
def listFilesWithNoParents(self, childBlockName):
"""
:param childBlockName:
:return:
"""
allFiles = self.dbs.listFiles(block_name=childBlockName)
parentFiles = self.dbs.listFileParents(block_name=childBlockName)
allFileNames = set()
for fInfo in allFiles:
allFileNames.add(fInfo['logical_file_name'])
cfile = set()
for pFile in parentFiles:
cfile.add(pFile['logical_file_name'])
noParentFiles = allFileNames - cfile
return list(noParentFiles)
def fixMissingParentageDatasets(self, childDataset, insertFlag=True):
"""
:param childDataset: child dataset need to set the parentage correctly.
:return: blocks which failed to insert parentage. for retry
"""
pDatasets = self.listDatasetParents(childDataset)
# print("parent datasets %s\n" % pDatasets)
# pDatasets format is
# [{'this_dataset': '/SingleMuon/Run2016D-03Feb2017-v1/MINIAOD', 'parent_dataset_id': 13265209, 'parent_dataset': '/SingleMuon/Run2016D-23Sep2016-v1/AOD'}]
if not pDatasets:
self.logger.warning("No parent dataset found for child dataset %s", childDataset)
return {}
blocks = self.listBlocksWithNoParents(childDataset)
failedBlocks = []
for blockName in blocks:
try:
numFiles = self.findAndInsertMissingParentage(blockName, insertFlag=insertFlag)
self.logger.debug("%s file parentage added for block %s" % (numFiles, blockName))
except Exception as ex:
self.logger.exception("Parentage updated failed for block %s", blockName)
failedBlocks.append(blockName)
return failedBlocks
def insertMissingParentageForAllFiles(self, childDataset, filterFilesWithParents=True, insertFlag=False):
"""
:param childDataset: child dataset need to set the parentage correctly.
:param filterFilesWithParents: if True, only select files without parents, if False all the files in the dataset
:param insertFlag: if True, insert to DBS, if False just get the list of the file parentage without insert
:return: blocks which failed to insert parentage. should be used for retrying
"""
blocks = [b['block_name'] for b in self.dbs.listBlocks(dataset=childDataset)]
failedBlocks = []
print("Handling %d blocks" % len(blocks))
totalFiles = 0
for blockName in blocks:
try:
if filterFilesWithParents:
childLFNs = self.listFilesWithNoParents(blockName)
if len(childLFNs) == 0:
continue
else:
childLFNs = []
numFiles = self.findAndInsertMissingParentage(blockName, childLFNs=childLFNs, insertFlag=insertFlag)
print("%s file parentage added for block %s" % (numFiles, blockName))
totalFiles += numFiles
except Exception as e:
print(traceback.format_exc())
failedBlocks.append(blockName)
print("Total pairs: ", totalFiles)
return failedBlocks